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Zammit M, Bartoli J, Kellenberger C, Melani P, Roussel A, Cascales E, Leone P. Structure-function analysis of PorX Fj, the PorX homolog from Flavobacterium johnsioniae, suggests a role of the CheY-like domain in type IX secretion motor activity. Sci Rep 2024; 14:6577. [PMID: 38503809 PMCID: PMC10951265 DOI: 10.1038/s41598-024-57089-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
The type IX secretion system (T9SS) is a large multi-protein transenvelope complex distributed into the Bacteroidetes phylum and responsible for the secretion of proteins involved in pathogenesis, carbohydrate utilization or gliding motility. In Porphyromonas gingivalis, the two-component system PorY sensor and response regulator PorX participate to T9SS gene regulation. Here, we present the crystal structure of PorXFj, the Flavobacterium johnsoniae PorX homolog. As for PorX, the PorXFj structure is comprised of a CheY-like N-terminal domain and an alkaline phosphatase-like C-terminal domain separated by a three-helix bundle central domain. While not activated and monomeric in solution, PorXFj crystallized as a dimer identical to active PorX. The CheY-like domain of PorXFj is in an active-like conformation, and PorXFj possesses phosphodiesterase activity, in agreement with the observation that the active site of its phosphatase-like domain is highly conserved with PorX.
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Affiliation(s)
- Mariotte Zammit
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Centre National de la Recherche Scientifique, Marseille, France
| | - Julia Bartoli
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Centre National de la Recherche Scientifique, Marseille, France
| | - Christine Kellenberger
- Laboratoire de Chimie Bactérienne (LCB, UMR7283), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Centre National de la Recherche Scientifique, Marseille, France
| | - Pauline Melani
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Centre National de la Recherche Scientifique, Marseille, France
| | - Alain Roussel
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Centre National de la Recherche Scientifique, Marseille, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Centre National de la Recherche Scientifique, Marseille, France
| | - Philippe Leone
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR7255), Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, Centre National de la Recherche Scientifique, Marseille, France.
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2
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Specific recognition of cyclic oligonucleotides by Cap4 for phage infection. Int J Biol Macromol 2023; 237:123656. [PMID: 36796558 DOI: 10.1016/j.ijbiomac.2023.123656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
Under selective pressure, bacteria have evolved diverse defense systems against phage infections. The SMODS-associated and fused to various effector domains (SAVED)-domain containing proteins were identified as major downstream effectors in cyclic oligonucleotide-based antiphage signaling system (CBASS) for bacterial defense. Recent study structurally characterizes a cGAS/DncV-like nucleotidyltransferase (CD-NTase)-associated protein 4 from Acinetobacter baumannii (AbCap4) in complex with 2'3'3'-cyclic AMP-AMP-AMP (cAAA). However, the homologue Cap4 from Enterobacter cloacae (EcCap4) is activated by 3'3'3'-cyclic AMP-AMP-GMP (cAAG). To elucidate the ligand specificity of Cap4 proteins, we determined the crystal structures of full-length wild-type and K74A mutant of EcCap4 to 2.18 and 2.42 Å resolution, respectively. The DNA endonuclease domain of EcCap4 shares similar catalytic mechanism with type II restriction endonuclease. Mutating the key residue K74 in the conserved DXn(D/E)XK motif completely abolishes its DNA degradation activity. The potential ligand-binding cavity of EcCap4 SAVED domain is located adjacent to its N-terminal domain, significantly differing from the centrally located cavity of AbCap4 SAVED domain which recognizes cAAA. Based on structural and bioinformatic analysis, we found that Cap4 proteins can be classified into two types: the type I Cap4, like AbCap4, recognize cAAA and the type II Cap4, like EcCap4, bind cAAG. Several conserved residues identified at the surface of potential ligand-binding pocket of EcCap4 SAVED domain are confirmed by ITC experiment for their direct binding roles for cAAG. Changing Q351, T391 and R392 to alanine abolished the binding of cAAG by EcCap4 and significantly reduced the anti-phage ability of the E. cloacae CBASS system constituting EcCdnD (CD-NTase in clade D) and EcCap4. In summary, we revealed the molecular basis for specific cAAG recognition by the C-terminal SAVED domain of EcCap4 and demonstrates the structural differences for ligand discrimination among different SAVED-domain containing proteins.
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Kishimoto H, Azai C, Yamamoto T, Mutoh R, Nakaniwa T, Tanaka H, Miyanoiri Y, Kurisu G, Oh-oka H. Soluble domains of cytochrome c-556 and Rieske iron-sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis. Curr Res Struct Biol 2023; 5:100101. [PMID: 37180033 PMCID: PMC10172866 DOI: 10.1016/j.crstbi.2023.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
In photosynthetic green sulfur bacteria, the electron transfer reaction from menaquinol:cytochrome c oxidoreductase to the P840 reaction center (RC) complex occurs directly without any involvement of soluble electron carrier protein(s). X-ray crystallography has determined the three-dimensional structures of the soluble domains of the CT0073 gene product and Rieske iron-sulfur protein (ISP). The former is a mono-heme cytochrome c with an α-absorption peak at 556 nm. The overall fold of the soluble domain of cytochrome c-556 (designated as cyt c-556sol) consists of four α-helices and is very similar to that of water-soluble cyt c-554 that independently functions as an electron donor to the P840 RC complex. However, the latter's remarkably long and flexible loop between the α3 and α4 helices seems to make it impossible to be a substitute for the former. The structure of the soluble domain of the Rieske ISP (Rieskesol protein) shows a typical β-sheets-dominated fold with a small cluster-binding and a large subdomain. The architecture of the Rieskesol protein is bilobal and belongs to those of b6f-type Rieske ISPs. Nuclear magnetic resonance (NMR) measurements revealed weak non-polar but specific interaction sites on Rieskesol protein when mixed with cyt c-556sol. Therefore, menaquinol:cytochrome c oxidoreductase in green sulfur bacteria features a Rieske/cytb complex tightly associated with membrane-anchored cyt c-556.
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Affiliation(s)
- Hiraku Kishimoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Chihiro Azai
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoya Yamamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Risa Mutoh
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tetsuko Nakaniwa
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
- Corresponding author.
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
- Corresponding author.
| | - Hirozo Oh-oka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
- Center for Education in Liberal Arts and Sciences, Osaka University, Toyonaka, Osaka, 560-0043, Japan
- Corresponding author. Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
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Fuchsbauer O, Lunar Silva I, Cascales E, Roussel A, Leone P. Structural and functional analyses of the Porphyromonas gingivalis type IX secretion system PorN protein. J Biol Chem 2022; 298:101618. [PMID: 35065963 PMCID: PMC8861641 DOI: 10.1016/j.jbc.2022.101618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Porphyromonas gingivalis, the major human pathogen bacterium associated with periodontal diseases, secretes virulence factors through the Bacteroidetes-specific type IX secretion system (T9SS). Effector proteins of the T9SS are recognized by the complex via their conserved C-terminal domains (CTDs). Among the 18 proteins essential for T9SS function in P. gingivalis, PorN is a periplasmic protein that forms large ring-shaped structures in association with the PorK outer membrane lipoprotein. PorN also mediates contacts with the PorM subunit of the PorLM energetic module, and with the effector’s CTD. However, no information is available on the PorN structure and on the implication of PorN domains for T9SS assembly and effector recognition. Here we present the crystal structure of PorN at 2.0-Å resolution, which represents a novel fold with no significant similarity to any known structure. In agreement with in silico analyses, we also found that the N- and C-terminal regions of PorN are intrinsically disordered. Our functional studies showed that the N-terminal disordered region is involved in PorN dimerization while the C-terminal disordered region is involved in the interaction with PorK. Finally, we determined that the folded PorN central domain is involved in the interaction with PorM, as well as with the effector’s CTD. Altogether, these results lay the foundations for a more comprehensive model of T9SS architecture and effector transport.
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Affiliation(s)
- Olivier Fuchsbauer
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, Marseille, France; Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, Marseille, France
| | - Ignacio Lunar Silva
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, Aix-Marseille Université - Centre National de la Recherche Scientifique (UMR7255), Marseille Cedex 20, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, Aix-Marseille Université - Centre National de la Recherche Scientifique (UMR7255), Marseille Cedex 20, France
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, Marseille, France; Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, Marseille, France
| | - Philippe Leone
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, Marseille, France; Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, Marseille, France.
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Crystal structures of ORFV125 provide insight into orf virus-mediated inhibition of apoptosis. Biochem J 2021; 477:4527-4541. [PMID: 33175095 PMCID: PMC7719400 DOI: 10.1042/bcj20200776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
Premature apoptosis of cells is a strategy utilized by multicellular organisms to counter microbial threats. Orf virus (ORFV) is a large double-stranded DNA virus belonging to the poxviridae. ORFV encodes for an apoptosis inhibitory protein ORFV125 homologous to B-cell lymphoma 2 or Bcl-2 family proteins, which has been shown to inhibit host cell encoded pro-apoptotic Bcl-2 proteins. However, the structural basis of apoptosis inhibition by ORFV125 remains to be clarified. We show that ORFV125 is able to bind to a range of peptides spanning the BH3 motif of human pro-apoptotic Bcl-2 proteins including Bax, Bak, Puma and Hrk with modest to weak affinity. We then determined the crystal structures of ORFV125 alone as well as bound to the highest affinity ligand Bax BH3 motif. ORFV125 adopts a globular Bcl-2 fold comprising 7 α-helices, and utilizes the canonical Bcl-2 binding groove to engage pro-apoptotic host cell Bcl-2 proteins. In contrast with a previously predicted structure, ORFV125 adopts a domain-swapped dimeric topology, where the α1 helix from one protomer is swapped into a neighbouring unit. Furthermore, ORFV125 differs from the conserved architecture of the Bcl-2 binding groove and instead of α3 helix forming one of the binding groove walls, ORFV125 utilizes an extended α2 helix that comprises the equivalent region of helix α3. This results in a subtle variation of previously observed dimeric Bcl-2 architectures in other poxvirus and human encoded Bcl-2 proteins. Overall, our results provide a structural and mechanistic basis for orf virus-mediated inhibition of host cell apoptosis.
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6
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Kanao T, Hase N, Nakayama H, Yoshida K, Nishiura K, Kosaka M, Kamimura K, Hirano Y, Tamada T. Reaction mechanism of tetrathionate hydrolysis based on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans. Protein Sci 2021; 30:328-338. [PMID: 33103311 PMCID: PMC7784748 DOI: 10.1002/pro.3984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 11/10/2022]
Abstract
Tetrathionate hydrolase (4THase) plays an important role in dissimilatory sulfur oxidation in the acidophilic iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans. The structure of recombinant 4THase from A. ferrooxidans (Af-Tth) was determined by X-ray crystallography to a resolution of 1.95 Å. Af-Tth is a homodimer, and its monomer structure exhibits an eight-bladed β-propeller motif. Two insertion loops participate in dimerization, and one loop forms a cavity with the β-propeller region. We observed unexplained electron densities in this cavity of the substrate-soaked structure. The anomalous difference map generated using diffraction data collected at a wavelength of 1.9 Å indicated the presence of polymerized sulfur atoms. Asp325, a highly conserved residue among 4THases, was located near the polymerized sulfur atoms. 4THase activity was completely abolished in the site-specific Af-Tth D325N variant, suggesting that Asp325 plays a crucial role in the first step of tetrathionate hydrolysis. Considering that the Af-Tth reaction occurs only under acidic pH, Asp325 acts as an acid for the tetrathionate hydrolysis reaction. The polymerized sulfur atoms in the active site cavity may represent the intermediate product in the subsequent step.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Naruki Hase
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Hisayuki Nakayama
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Kyoya Yoshida
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Kazumi Nishiura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Megumi Kosaka
- Department of Instrumental Analysis, Advanced Science Research CenterOkayama UniversityOkayamaJapan
| | - Kazuo Kamimura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Yu Hirano
- Institute for Quantum Life ScienceNational Institutes for Quantum and Radiological Science and TechnologyTokaiJapan
| | - Taro Tamada
- Institute for Quantum Life ScienceNational Institutes for Quantum and Radiological Science and TechnologyTokaiJapan
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7
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Trinh NTT, Tran HQ, Van Dong Q, Cambillau C, Roussel A, Leone P. Crystal structure of Type IX secretion system PorE C-terminal domain from Porphyromonas gingivalis in complex with a peptidoglycan fragment. Sci Rep 2020; 10:7384. [PMID: 32355178 PMCID: PMC7192894 DOI: 10.1038/s41598-020-64115-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Porphyromonas gingivalis, the major human pathogen associated to periodontal diseases, utilizes the Bacteroidetes-specific type IX secretion system (T9SS) to export virulence factors. PorE is a periplasmic multi-domain lipoprotein associated to the outer membrane that was recently identified as essential for T9SS function. Little is known on T9SS at the structural level, and in particular its interaction with peptidoglycan. This prompted us to carry out structural studies on PorE full length as well as on its four isolated domains. Here we report the crystal structure of the C-terminal OmpA_C-like putative peptidoglycan-binding domain at 1.55 Å resolution. An electron density volume was identified in the protein cleft, making it possible to build a naturally-occurring peptidoglycan fragment. This result suggests that PorE interacts with peptidoglycan and that PorE could anchor T9SS to the cell wall.
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Affiliation(s)
- Nhung Thi Trang Trinh
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Faculty of Medical Technology, PHENIKAA University, Yen Nghia, Ha Dong, Hanoi 12116, Vietnam.,PHENIKAA Research and Technology Institute (PRATI), A&A Green Phoenix Group JSC, No. 167 Hoang Ngan, Trung Hoa, Cau Giay, Hanoi 11313, Vietnam
| | - Hieu Quang Tran
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France
| | - Quyen Van Dong
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 18 Hoang Quoc Viet, Ha Noi, Vietnam.,University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 18 Hoang Quoc Viet, Ha Noi, Vietnam
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France
| | - Philippe Leone
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France. .,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, 163 Avenue de Luminy, Case 932, 13009, Marseille, France.
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Doyle L, Ovchinnikova OG, Myler K, Mallette E, Huang BS, Lowary TL, Kimber MS, Whitfield C. Biosynthesis of a conserved glycolipid anchor for Gram-negative bacterial capsules. Nat Chem Biol 2019; 15:632-640. [DOI: 10.1038/s41589-019-0276-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/25/2019] [Indexed: 11/09/2022]
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9
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Jang Y, Choi G, Hong S, Jo I, Ahn J, Choi SH, Ha NC. A Novel Tetrameric Assembly Configuration in VV2_1132, a LysR-Type Transcriptional Regulator in Vibrio vulnificus. Mol Cells 2018; 41:301-310. [PMID: 29487273 PMCID: PMC5935101 DOI: 10.14348/molcells.2018.2190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/03/2017] [Accepted: 01/08/2018] [Indexed: 01/22/2023] Open
Abstract
LysR-type transcriptional regulators (LTTRs) contain an N-terminal DNA binding domain (DBD) and a C-terminal regulatory domain (RD). Typically, LTTRs function as homotetramers. VV2_1132 was identified in Vibrio vulnificus as an LTTR that is a homologue of HypT (also known as YjiE or QseD) in Escherichia coli. In this study, we determined the crystal structure of full-length VV2_1132 at a resolution of 2.2 Å, thereby revealing a novel combination of the domains in the tetrameric assembly. Only one DBD dimer in the tetramer can bind to DNA, because the DNA binding motifs of the other DBD dimer are completely buried in the tetrameric assembly. Structural and functional analyses of VV2_1132 suggest that it might not perform the same role as E. coli HypT, indicating that further study is required to elucidate the function of this gene in V. vulnificus. The unique structure of VV2_1132 extends our knowledge of LTTR function and mechanisms of action.
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Affiliation(s)
- Yongdae Jang
- Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Garam Choi
- Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea
- National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Seokho Hong
- Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Inseong Jo
- Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Jinsook Ahn
- Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Sang Ho Choi
- Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea
- National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, Seoul 08826, Korea
| | - Nam-Chul Ha
- Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea
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Abstract
TSPO is a 18 kDa membrane protein that exists in mammalian as two isoforms 1 and 2. They are involved in different functions and are located in different membranes. TSPO1 is mainly located in outer mitochondrial membrane, whereas TSPO2 is encountered in plasma membrane of red blood cells. Determination of their structures is a milestone to understand their function. Their natural abundance is not sufficient to get large amounts usually required for structural studies. We described heterologous overexpression in both bacterial and cell-free system and purification on immobilized-metal affinity chromatography (IMAC) of both proteins. Using the same vector, TSPO1 is mostly recovered in bacterial inclusion bodies whereas TSPO2 is found in both bacterial cytosol and inclusion bodies, but in low amounts. Cell-free expression was the best system to overexpress pure TSPO2.
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Abstract
Par-4 is a unique proapoptotic protein with the ability to induce apoptosis selectively in cancer cells. The X-ray crystal structure of the C-terminal domain of Par-4 (Par-4CC), which regulates its apoptotic function, was obtained by MAD phasing. Par-4 homodimerizes by forming a parallel coiled-coil structure. The N-terminal half of Par-4CC contains the homodimerization subdomain. This structure includes a nuclear export signal (Par-4NES) sequence, which is masked upon dimerization indicating a potential mechanism for nuclear localization. The heteromeric-interaction models specifically showed that charge interaction is an important factor in the stability of heteromers of the C-terminal leucine zipper subdomain of Par-4 (Par-4LZ). These heteromer models also displayed NES masking capacity and therefore the ability to influence intracellular localization.
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12
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Myung Choi J, Cao TP, Wouk Kim S, Ho Lee K, Haeng Lee S. MxaJ structure reveals a periplasmic binding protein-like architecture with unique secondary structural elements. Proteins 2017; 85:1379-1386. [DOI: 10.1002/prot.25283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Jin Myung Choi
- Department of Cellular and Molecular Medicine; Chosun University School of Medicine; Gwangju 61452 Korea
| | - Thinh-Phat Cao
- Department of Cellular and Molecular Medicine; Chosun University School of Medicine; Gwangju 61452 Korea
- National Research Center for Dementia, Chosun University; Gwangju 61452 Korea
| | - Si Wouk Kim
- Department of Environmental Engineering; Chosun University; Gwangju 61452 Korea
| | - Kun Ho Lee
- National Research Center for Dementia, Chosun University; Gwangju 61452 Korea
| | - Sung Haeng Lee
- Department of Cellular and Molecular Medicine; Chosun University School of Medicine; Gwangju 61452 Korea
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13
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Faille A, Gavalda S, Slama N, Lherbet C, Maveyraud L, Guillet V, Laval F, Quémard A, Mourey L, Pedelacq JD. Insights into Substrate Modification by Dehydratases from Type I Polyketide Synthases. J Mol Biol 2017; 429:1554-1569. [PMID: 28377293 DOI: 10.1016/j.jmb.2017.03.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/21/2017] [Accepted: 03/27/2017] [Indexed: 02/04/2023]
Abstract
Dehydration reactions play a crucial role in the de novo biosynthesis of fatty acids and a wide range of pharmacologically active polyketide natural products with strong emphasis on human medicine. The type I polyketide synthase PpsC from Mycobacterium tuberculosis catalyzes key biosynthetic steps of lipid virulence factors phthiocerol dimycocerosates and phenolic glycolipids. Given the insolubility of the natural C28-C30 fatty acyl substrate of the PpsC dehydratase (DH) domain, we investigated its structure-function relationships in the presence of shorter surrogate substrates. Since most enzymes belonging to the (R)-specific enoyl hydratase/hydroxyacyl dehydratase family conduct the reverse hydration reaction in vitro, we have determined the X-ray structures of the PpsC DH domain, both unliganded (apo) and in complex with trans-but-2-enoyl-CoA or trans-dodec-2-enoyl-CoA derivatives. This study provides for the first time a snapshot of dehydratase-ligand interactions following a hydration reaction. Our structural analysis allowed us to identify residues essential for substrate binding and activity. The structural comparison of the two complexes also sheds light on the need for long acyl chains for this dehydratase to carry out its function, consistent with both its in vitro catalytic behavior and the physiological role of the PpsC enzyme.
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Affiliation(s)
- Alexandre Faille
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Sabine Gavalda
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Nawel Slama
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | | | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Valérie Guillet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Françoise Laval
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France.
| | - Jean-Denis Pedelacq
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France.
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14
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Mihelič M, Vlahoviček-Kahlina K, Renko M, Mesnage S, Doberšek A, Taler-Verčič A, Jakas A, Turk D. The mechanism behind the selection of two different cleavage sites in NAG-NAM polymers. IUCRJ 2017; 4:185-198. [PMID: 28250957 PMCID: PMC5330529 DOI: 10.1107/s2052252517000367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by β-(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucos-aminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers. In spite of more than fifty years of structural studies of lysozyme, it is still not known how the enzyme selects the bond to be cleaved. Using macromolecular crystallography, chemical synthesis and molecular modelling, this study explains how these two groups of enzymes based on an equivalent structural core exhibit a difference in selectivity. The crystal structures of Staphylococcus aureusN-acetylglucosaminidase autolysin E (AtlE) alone and in complex with fragments of peptidoglycan revealed that N-acetylglucosaminidases and muramidases approach the substrate at alternate glycosidic bond positions from opposite sides. The recognition pocket for NAM residues in the active site of N-acetylglucosaminidases may make them a suitable drug target.
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Affiliation(s)
- Marko Mihelič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | | | - Miha Renko
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Stephane Mesnage
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, England
| | - Andreja Doberšek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Ajda Taler-Verčič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Andreja Jakas
- Division of Organic Chemistry, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
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15
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Lee IM, Tu IF, Yang FL, Ko TP, Liao JH, Lin NT, Wu CY, Ren CT, Wang AHJ, Chang CM, Huang KF, Wu SH. Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage ΦAB6 tailspike protein. Sci Rep 2017; 7:42711. [PMID: 28209973 PMCID: PMC5314372 DOI: 10.1038/srep42711] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/12/2017] [Indexed: 12/24/2022] Open
Abstract
With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeutic to combat bacterial infection. Herein, we characterize the bacteriophage ΦAB6 tailspike protein (TSP), which specifically hydrolyzed the EPS of A. baumannii strain 54149 (Ab-54149). Ab-54149 EPS exhibited the same chemical structure as two antibiotic-resistant A. baumannii strains. The ΦAB6 TSP-digested products comprised oligosaccharides of two repeat units, typically with stoichiometric pseudaminic acid (Pse). The 1.48-1.89-Å resolution crystal structures of an N-terminally-truncated ΦAB6 TSP and its complexes with the semi-hydrolyzed products revealed a trimeric β-helix architecture that bears intersubunit carbohydrate-binding grooves, with some features unusual to the TSP family. The structures suggest that Pse in the substrate is an important recognition site for ΦAB6 TSP. A region in the carbohydrate-binding groove is identified as the determinant of product specificity. The structures also elucidated a retaining mechanism, for which the catalytic residues were verified by site-directed mutagenesis. Our findings provide a structural basis for engineering the enzyme to produce desired oligosaccharides, which is useful for the development of glycoconjugate vaccines against A. baumannii infection.
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Affiliation(s)
- I-Ming Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Core Facilities for Protein Structural Analysis (CFPSA), Academia Sinica, Taipei 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Nien-Tsung Lin
- Master program in Microbiology and Immunology, Tzu Chi University, Hualien 970, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chien-Tai Ren
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Core Facilities for Protein Structural Analysis (CFPSA), Academia Sinica, Taipei 115, Taiwan
| | - Ching-Ming Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Core Facilities for Protein Structural Analysis (CFPSA), Academia Sinica, Taipei 115, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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16
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The MPN domain of Caenorhabditis elegans UfSP modulates both substrate recognition and deufmylation activity. Biochem Biophys Res Commun 2016; 476:450-456. [PMID: 27240952 DOI: 10.1016/j.bbrc.2016.05.143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 05/27/2016] [Indexed: 02/05/2023]
Abstract
Ubiquitin-fold modifier 1 (Ufm1) specific protease (UfSP) is a novel cysteine protease that activates Ufm1 from its precursor by processing the C-terminus to expose the conserved Gly necessary for substrate conjugation and de-conjugates Ufm1 from the substrate. There are two forms: UfSP1 and UfSP2, the later with an additional domain at the N-terminus. Ufm1 and both the conjugating and deconjugating enzymes are highly conserved. However, in Caenorhabditis elegans there is one UfSP which has extra 136 residues at the N terminus compared to UfSP2. The crystal structure of cUfSP reveals that these additional residues display a MPN fold while the rest of the structure mimics that of UfSP2. The MPN domain does not have the metalloprotease activity found in some MPN-domain containing protein, rather it is required for the recognition and deufmylation of the substrate of cUfSP, UfBP1. In addition, the MPN domain is also required for localization to the endoplasmic reticulum.
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17
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Bacterial β-Kdo glycosyltransferases represent a new glycosyltransferase family (GT99). Proc Natl Acad Sci U S A 2016; 113:E3120-9. [PMID: 27199480 DOI: 10.1073/pnas.1603146113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Kdo (3-deoxy-d-manno-oct-2-ulosonic acid) is an eight-carbon sugar mostly confined to Gram-negative bacteria. It is often involved in attaching surface polysaccharides to their lipid anchors. α-Kdo provides a bridge between lipid A and the core oligosaccharide in all bacterial LPSs, whereas an oligosaccharide of β-Kdo residues links "group 2" capsular polysaccharides to (lyso)phosphatidylglycerol. β-Kdo is also found in a small number of other bacterial polysaccharides. The structure and function of the prototypical cytidine monophosphate-Kdo-dependent α-Kdo glycosyltransferase from LPS assembly is well characterized. In contrast, the β-Kdo counterparts were not identified as glycosyltransferase enzymes by bioinformatics tools and were not represented among the 98 currently recognized glycosyltransferase families in the Carbohydrate-Active Enzymes database. We report the crystallographic structure and function of a prototype β-Kdo GT from WbbB, a modular protein participating in LPS O-antigen synthesis in Raoultella terrigena The β-Kdo GT has dual Rossmann-fold motifs typical of GT-B enzymes, but extensive deletions, insertions, and rearrangements result in a unique architecture that makes it a prototype for a new GT family (GT99). The cytidine monophosphate-binding site in the C-terminal α/β domain closely resembles the corresponding site in bacterial sialyltransferases, suggesting an evolutionary connection that is not immediately evident from the overall fold or sequence similarities.
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18
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Tongsook C, Uhl MK, Jankowitsch F, Mack M, Gruber K, Macheroux P. Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-d-riboflavin to the antibiotic roseoflavin. FEBS J 2016; 283:1531-49. [PMID: 26913589 PMCID: PMC4982073 DOI: 10.1111/febs.13690] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/26/2016] [Accepted: 02/18/2016] [Indexed: 11/28/2022]
Abstract
N,N‐8‐demethyl‐8‐amino‐d‐riboflavin dimethyltransferase (RosA) catalyses the final dimethylation of 8‐demethyl‐8‐amino‐d‐riboflavin (AF) to the antibiotic roseoflavin (RoF) in Streptomyces davawensis. In the present study, we solved the X‐ray structure of RosA, and determined the binding properties of substrates and products. Moreover, we used steady‐state and rapid reaction kinetic studies to obtain detailed information on the reaction mechanism. The structure of RosA was found to be similar to that of previously described S‐adenosylmethionine (SAM)‐dependent methyltransferases, featuring two domains: a mainly α‐helical ‘orthogonal bundle’ and a Rossmann‐like domain (α/β twisted open sheet). Bioinformatics studies and molecular modelling enabled us to predict the potential SAM and AF binding sites in RosA, suggesting that both substrates, AF and SAM, bind independently to their respective binding pocket. This finding was confirmed by kinetic experiments that demonstrated a random‐order ‘bi‐bi’ reaction mechanism. Furthermore, we determined the dissociation constants for substrates and products by either isothermal titration calorimetry or UV/Vis absorption spectroscopy, revealing that both products, RoF and S‐adenosylhomocysteine (SAH), bind more tightly to RosA compared with the substrates, AF and SAM. This suggests that RosA may contribute to roseoflavin resistance in S. davawensis. The tighter binding of products is also reflected by the results of inhibition experiments, in which RoF and SAH behave as competitive inhibitors for AF and SAM, respectively. We also showed that formation of a ternary complex of RosA, RoF and SAH (or SAM) leads to drastic spectral changes that are indicative of a hydrophobic environment. Database Structural data are available in the Protein Data Bank under accession number 4D7K.
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Affiliation(s)
| | - Michael K Uhl
- Institute of Molecular Biosciences, University of Graz, Austria
| | - Frank Jankowitsch
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Matthias Mack
- Department of Biotechnology, Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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19
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Davidov G, Müller FD, Baumgartner J, Bitton R, Faivre D, Schüler D, Zarivach R. Crystal structure of the magnetobacterial protein MtxA C-terminal domain reveals a new sequence-structure relationship. Front Mol Biosci 2015; 2:25. [PMID: 26052516 PMCID: PMC4439547 DOI: 10.3389/fmolb.2015.00025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/04/2015] [Indexed: 01/07/2023] Open
Abstract
Magnetotactic bacteria (MTB) are a diverse group of aquatic bacteria that have the magnetotaxis ability to align themselves along the geomagnetic field lines and to navigate to a microoxic zone at the bottom of chemically stratified natural water. This special navigation is the result of a unique linear assembly of a specialized organelle, the magnetosome, which contains a biomineralized magnetic nanocrystal enveloped by a cytoplasmic membrane. The Magnetospirillum gryphiswaldense MtxA protein (MGR_0208) was suggested to play a role in bacterial magnetotaxis due to its gene location in an operon together with putative signal transduction genes. Since no homology is found for MtxA, and to better understand the role and function of MtxA in MTBés magnetotaxis, we initiated structural and functional studies of MtxA via X-ray crystallography and deletion mutagenesis. Here, we present the crystal structure of the MtxA C-terminal domain and provide new insights into its sequence-structure relationship.
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Affiliation(s)
- Geula Davidov
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the NegevBeer Sheva, Israel
| | - Frank D. Müller
- Department of Microbiology, University of BayreuthBayreuth, Germany
| | - Jens Baumgartner
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces (MPI)Potsdam, Germany
| | - Ronit Bitton
- Department of Chemical Engineering, Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the NegevBeer-Sheva, Israel
| | - Damien Faivre
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces (MPI)Potsdam, Germany
| | - Dirk Schüler
- Department of Microbiology, University of BayreuthBayreuth, Germany
| | - Raz Zarivach
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the NegevBeer Sheva, Israel,*Correspondence: Raz Zarivach, Department of Life Sciences, Ben Gurion University of the Negev, PO Box. 653, Beer-Sheva 84105, Israel
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20
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Choi JM, Choi YH, Sudhanva MS, Devakumar S, Lee KH, Cha JH, Lee SH. Crystal structure of CagL from Helicobacter pylori K74 strain. Biochem Biophys Res Commun 2015; 460:964-70. [DOI: 10.1016/j.bbrc.2015.03.135] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 01/01/2023]
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21
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The Crystal Structure of Siroheme Decarboxylase in Complex with Iron-Uroporphyrin III Reveals Two Essential Histidine Residues. J Mol Biol 2014; 426:3272-3286. [DOI: 10.1016/j.jmb.2014.07.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/11/2014] [Accepted: 07/17/2014] [Indexed: 11/18/2022]
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22
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Fukumura T, Furukawa Y, Kawaguchi T, Saijo-Hamano Y, Namba K, Imada K, Minamino T. Crystallization and preliminary X-ray analysis of the periplasmic domain of FliP, an integral membrane component of the bacterial flagellar type III protein-export apparatus. Acta Crystallogr F Struct Biol Commun 2014; 70:1215-8. [PMID: 25195894 PMCID: PMC4157421 DOI: 10.1107/s2053230x14014678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/21/2014] [Indexed: 11/11/2022] Open
Abstract
The bacterial flagellar proteins are transported via a specific export apparatus to the distal end of the growing structure for their self-assembly. FliP is an essential membrane component of the export apparatus. FliP has an N-terminal signal peptide and is predicted to have four transmembrane (TM) helices and a periplasmic domain (FliPP) between TM-2 and TM-3. In this study, FliPP from Thermotoga maritima (TmFliPP) and its selenomethionine derivative (SeMet-TmFliPP) were purified and crystallized. TmFliPP formed a homotetramer in solution. Crystals of TmFliPP and SeMet-TmFliPP were obtained by the hanging-drop vapour-diffusion technique with 2-methyl-2,4-pentanediol as a precipitant. These two crystals grew in the hexagonal space group P6222 or P6422, with unit-cell parameters a = b = 114.9, c = 193.8 Å. X-ray diffraction data were collected from crystals of TmFliPP and SeMet-TmFliPP to 2.4 and 2.8 Å resolution, respectively.
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Affiliation(s)
- Takuma Fukumura
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsuya Kawaguchi
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yumiko Saijo-Hamano
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Riken Quantitative Biology Center, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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23
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Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature 2014; 510:422-426. [PMID: 24814345 PMCID: PMC4066111 DOI: 10.1038/nature13263] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/14/2014] [Indexed: 12/24/2022]
Abstract
2-Oxoglutarate (2OG)-dependent oxygenases play important roles in the regulation of gene expression via demethylation of N-methylated chromatin components1,2, hydroxylation of transcription factors3, and of splicing factor proteins4. Recently, 2OG-oxygenases that catalyze hydroxylation of tRNA5-7 and ribosomal proteins8, have been shown to play roles in translation relating to cellular growth, TH17-cell differentiation and translational accuracy9-12. The finding that the ribosomal oxygenases (ROX) occur in organisms ranging from prokaryotes to humans8 raises questions as to their structural and evolutionary relationships. In Escherichia coli, ycfD catalyzes arginine-hydroxylation in the ribosomal protein L16; in humans, Mina53 (MYC-induced nuclear antigen) and NO66 (Nucleolar protein 66) catalyze histidine-hydroxylation in ribosomal proteins rpL27a and rpL8, respectively. The functional assignments of the ROX open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in residue- and protein-selectivities of prokaryotic and eukaryotic ROX, crystal structures of ycfD and ycfDRM from E. coli and Rhodothermus marinus with those of human Mina53 and NO66 (hROX) reveal highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-oxygenases. ROX structures in complex with/without their substrates, support their functional assignments as hydroxylases, but not demethylases and reveal how the subfamily has evolved to catalyze the hydroxylation of different residue sidechains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-hydroxylases including the hypoxia-inducible factor asparaginyl-hydroxylase (FIH) and histone Nε-methyl lysine demethylases (KDMs) identifies branchpoints in 2OG-oxygenase evolution and distinguishes between JmjC-hydroxylases and -demethylases catalyzing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate oxidizing species reacts. This coordination flexibility has likely contributed to the evolution of the wide range of reactions catalyzed by iron-oxygenases.
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24
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Jiang T, Chan HC, Huang CH, Ko TP, Huang TY, Liu JR, Guo RT. Substrate binding to a GH131 β-glucanase catalytic domain from Podospora anserina. Biochem Biophys Res Commun 2013; 438:193-7. [PMID: 23880343 DOI: 10.1016/j.bbrc.2013.07.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 07/14/2013] [Indexed: 11/15/2022]
Abstract
β-Glucanases have been utilized widely in industry to treat various carbohydrate-containing materials. Recently, the Podospora anserina β-glucanase 131A (PaGluc131A) was identified and classified to a new glycoside hydrolases GH131 family. It shows exo-β-1,3/exo-β-1,6 and endo-β-1,4 glucanase activities with a broad substrate specificity for laminarin, curdlan, pachyman, lichenan, pustulan, and cellulosic derivatives. Here we report the crystal structures of the PaGluc131A catalytic domain with or without ligand (cellotriose) at 1.8Å resolution. The cellotriose was clearly observed to occupy the +1 to +3 subsites in substrate binding cleft. The broadened substrate binding groove may explain the diverse substrate specificity. Based on our crystal structures, the GH131 family enzyme is likely to carry out the hydrolysis through an inverting catalytic mechanism, in which E99 and E139 are supposed to serve as the general base and general acid.
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Affiliation(s)
- Tong Jiang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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25
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De la Mora-Rey T, Guenther BD, Finzel BC. The structure of the TOG-like domain of Drosophila melanogaster Mast/Orbit. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:723-9. [PMID: 23832196 PMCID: PMC3702313 DOI: 10.1107/s1744309113015182] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/01/2013] [Indexed: 11/10/2022]
Abstract
Mast/Orbit is a nonmotor microtubule-associated protein (MAP) present in Drosophila melanogaster that reportedly binds microtubules at the plus end and is essential for mitosis. Sequence analysis has shown that the N-terminal domain (Mast-M1) resembles TOG domains from the Dis1-TOG family of proteins and stands as a representative of one of the three subclasses of divergent TOG-like domains (TOGL1) that includes human CLASP1. The crystal structure of Mast-M1 has been determined at 2.0 Å resolution and provides the first detailed structural description of any TOG-like domain. The structure confirms that Mast-M1 adopts a similar fold to the previously described Dis1-TOG domains of microtubule-binding proteins. A comparison with three known TOG-domain structures from XMAP215/Dis1 family members exposes significant differences between Mast-M1 and other TOG-domain structures in key residues at the proposed tubulin-binding edge.
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Affiliation(s)
- Teresa De la Mora-Rey
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, USA
| | - Brian D. Guenther
- Department of Diagnostic/Biological Sciences, University of Minnesota, 515 Delaware Street SE, Moos Tower, Minneapolis, MN 55455, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, USA
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Chang YM, Chen CKM, Ko TP, Chang-Chien MW, Wang AHJ. Structural analysis of the antibiotic-recognition mechanism of MarR proteins. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1138-49. [PMID: 23695258 DOI: 10.1107/s0907444913007117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 03/14/2013] [Indexed: 11/11/2022]
Abstract
Staphylococci cause a wide range of diseases in humans and animals, and the proteins of the multiple antibiotic-resistance repressor (MarR) family in staphylococci function as regulators of protein expression and confer resistance to multiple antibiotics. Diverse mechanisms such as biofilm formation, drug transport, drug modification etc. are associated with this resistance. In this study, crystal structures of the Staphylococcus aureus MarR homologue SAR2349 and its complex with salicylate and the aminoglycoside antibiotic kanamycin have been determined. The structure of SAR2349 shows for the first time that a MarR protein can interact directly with different classes of ligands simultaneously and highlights the importance and versatility of regulatory systems in bacterial antibiotic resistance. The three-dimensional structures of TcaR from S. epidermidis in complexes with chloramphenicol and with the aminoglycoside antibiotic streptomycin were also investigated. The crystal structures of the TcaR and SAR2349 complexes illustrate a general antibiotic-regulated resistance mechanism that may extend to other MarR proteins. To reveal the regulatory mechanism of the MarR proteins, the protein structures of this family were further compared and three possible mechanisms of regulation are proposed. These results are of general interest because they reveal a remarkably broad spectrum of ligand-binding modes of the multifunctional MarR proteins. This finding provides further understanding of antimicrobial resistance mechanisms in pathogens and strategies to develop new therapies against pathogens.
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Affiliation(s)
- Yu Ming Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
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27
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Saijo-Hamano Y, Matsunami H, Namba K, Imada K. Expression, purification, crystallization and preliminary X-ray diffraction analysis of a core fragment of FlgG, a bacterial flagellar rod protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:547-50. [PMID: 23695574 PMCID: PMC3660898 DOI: 10.1107/s1744309113008075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 03/24/2013] [Indexed: 11/10/2022]
Abstract
FlgG is a bacterial flagellar rod protein and constructs the distal rod connecting to the hook. FlgG of Salmonella enterica serovar Typhimurium is a 260-amino-acid protein composed of a folded core region and N- and C-terminal regions that are unfolded in solution. A core fragment of FlgG (FlgG47-227) was expressed, purified and crystallized. Crystals of native and SeMet-labelled FlgG47-227 were obtained by the sitting-drop vapour-diffusion technique with PEG MME 2000 as precipitant. The native crystal belonged to the primitive orthorhombic space group P212121, with unit-cell parameters a = 47.78, b = 68.94, c = 110.57 Å. The SeMet crystal also belonged to space group P212121, with unit-cell parameters a = 47.53, b = 67.04, c = 110.27 Å.
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Affiliation(s)
- Yumiko Saijo-Hamano
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hideyuki Matsunami
- Trans-Membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa 904-0412, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Riken Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumi Imada
- Department of Macromolecular Sciences, Graduate School of Sciences, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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28
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Hofmeyer T, Schmelz S, Degiacomi MT, Dal Peraro M, Daneschdar M, Scrima A, van den Heuvel J, Heinz DW, Kolmar H. Arranged sevenfold: structural insights into the C-terminal oligomerization domain of human C4b-binding protein. J Mol Biol 2012; 425:1302-17. [PMID: 23274142 DOI: 10.1016/j.jmb.2012.12.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/18/2012] [Accepted: 12/20/2012] [Indexed: 10/27/2022]
Abstract
The complement system as a major part of innate immunity is the first line of defense against invading microorganisms. Orchestrated by more than 60 proteins, its major task is to discriminate between host cells and pathogens and to initiate immune response. Additional recognition of necrotic or apoptotic cells demands a fine-tune regulation of this powerful system. C4b-binding protein (C4BP) is the major inhibitor of the classical complement and lectin pathway. The crystal structure of the human C4BP oligomerization domain in its 7α isoform and molecular simulations provide first structural insights of C4BP oligomerization. The heptameric core structure is stabilized by intermolecular disulfide bonds. In addition, thermal shift assays indicate that layers of electrostatic interactions mainly contribute to the extraordinary thermodynamic stability of the complex. These findings make C4BP a promising scaffold for multivalent ligand display with applications in immunology and biological chemistry.
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Affiliation(s)
- Thomas Hofmeyer
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Petersenstraße 22, 64287 Darmstadt, Germany
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29
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Xu N, Yu S, Moniot S, Weyand M, Blankenfeldt W. Crystallization and preliminary crystal structure analysis of the ligand-binding domain of PqsR (MvfR), the Pseudomonas quinolone signal (PQS) responsive quorum-sensing transcription factor of Pseudomonas aeruginosa. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1034-9. [PMID: 22949189 PMCID: PMC3433192 DOI: 10.1107/s1744309112032538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/17/2012] [Indexed: 01/17/2023]
Abstract
The opportunistic bacterial pathogen Pseudomonas aeruginosa employs three transcriptional regulators, LasR, RhlR and PqsR, to control the transcription of a large subset of its genes in a cell-density-dependent process known as quorum sensing. Here, the recombinant production, crystallization and structure solution of the ligand-binding domain of PqsR (MvfR), the LysR-type transcription factor that responds to the Pseudomonas quinolone signal (PQS), a quinolone-based quorum-sensing signal that is unique to P. aeruginosa and possibly a small number of other bacteria, is reported. PqsR regulates the expression of many virulence genes and may therefore be an interesting drug target. The ligand-binding domain (residues 91-319) was produced as a fusion with SUMO, and hexagonal-shaped crystals of purified PqsR_91-319 were obtained using the vapour-diffusion method. Crystallization in the presence of a PQS precursor allowed data collection to 3.25 Å resolution on a synchrotron beamline, and initial phases have been obtained using single-wavelength anomalous diffraction data from seleno-L-methionine-labelled crystals, revealing the space group to be P6(5)22, with unit-cell parameters a = b = 116-120, c = 115-117 Å.
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Affiliation(s)
- Ningna Xu
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Shen Yu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sébastien Moniot
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Michael Weyand
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Wulf Blankenfeldt
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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30
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Crystal structure of ISG54 reveals a novel RNA binding structure and potential functional mechanisms. Cell Res 2012; 22:1328-38. [PMID: 22825553 PMCID: PMC3434343 DOI: 10.1038/cr.2012.111] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Interferon-stimulated gene 56 (ISG56) family members play important roles in blocking viral replication and regulating cellular functions, however, their underlying molecular mechanisms are largely unclear. Here, we present the crystal structure of ISG54, an ISG56 family protein with a novel RNA-binding structure. The structure shows that ISG54 monomers have 9 tetratricopeptide repeat-like motifs and associate to form domain-swapped dimers. The C-terminal part folds into a super-helical structure and has an extensively positively-charged nucleotide-binding channel on its inner surface. EMSA results show that ISG54 binds specifically to some RNAs, such as adenylate uridylate (AU)-rich RNAs, with or without 5' triphosphorylation. Mutagenesis and functional studies show that this RNA-binding ability is important to its antiviral activity. Our results suggest a new mechanism underlying the antiviral activity of this interferon-inducible gene 56 family member.
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31
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Huang YH, Liu XY, Du XX, Jiang ZF, Su XD. The structural basis for the sensing and binding of cyclic di-GMP by STING. Nat Struct Mol Biol 2012; 19:728-30. [PMID: 22728659 DOI: 10.1038/nsmb.2333] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 05/22/2012] [Indexed: 12/17/2022]
Abstract
STING (stimulator of interferon genes) is an essential signaling adaptor that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). STING's structure and its binding mechanism to cyclic dinucleotides were unknown. We report here the crystal structures of the STING cytoplasmic domain and its complex with c-di-GMP, thus providing the structural basis for understanding STING function.
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Affiliation(s)
- Yi-He Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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32
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Structure of the carboxy-terminal region of a KCNH channel. Nature 2012; 481:530-3. [PMID: 22230959 PMCID: PMC3267858 DOI: 10.1038/nature10735] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Accepted: 11/23/2011] [Indexed: 11/15/2022]
Abstract
The KCNH family of ion channels, comprising ether-à-go-go (EAG), EAG-related gene (ERG), and EAG-like (ELK) K+ channel subfamilies, is crucial for repolarization of the cardiac action potential1, regulation of neuronal excitability2, and proliferation of tumor cells3. The C-terminal region of KCNH channels contains a cyclic nucleotide-binding homology domain (CNBHD) and C-linker that couples the CNBHD to the pore4. The C-linker/CNBHD is essential for proper function and trafficking of ion channels in the KCNH family5–9. However, despite the importance of the C-linker/CNBHD for the function of KCNH channels, the structural basis of ion channel regulation by the C-linker/CNBHD is unknown. Here we report the crystal structure of the C-linker/CNBHD of zebrafish ELK channels at 2.2 Å resolution. While the overall structure of the C-linker/CNBHD of zELK channels is similar to the cyclic nucleotide-binding domain (CNBD) structure of the related HCN channels10, there are dramatic differences. Unlike the CNBD of HCN, the CNBHD of zELK displays a negatively charged electrostatic profile that explains the lack of binding and regulation of KCNH channels by cyclic nucleotides4,11. Instead of cyclic nucleotide, the binding pocket is occupied by a short β-strand. Mutations of the β-strand shift the voltage dependence of activation to more depolarized voltages, implicating the β-strand as an intrinsic ligand for the CNBHD of zELK channels. In both zELK and HCN channels the C-linker is the site of virtually all of the intersubunit interactions in the C-terminal region. However, in the zELK structure there is a reorientation in the C-linker so the subunits form dimers instead of tetramers as observed in HCN channels. These results provide a structural framework for understanding the regulation of ion channels in the KCNH family by the C-linker/CNBHD and may guide the design of specific drugs.
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33
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Gehret JJ, Gu L, Geders TW, Brown WC, Gerwick L, Gerwick WH, Sherman DH, Smith JL. Structure and activity of DmmA, a marine haloalkane dehalogenase. Protein Sci 2012; 21:239-48. [PMID: 22124946 DOI: 10.1002/pro.2009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/16/2011] [Accepted: 11/23/2011] [Indexed: 11/07/2022]
Abstract
DmmA is a haloalkane dehalogenase (HLD) identified and characterized from the metagenomic DNA of a marine microbial consortium. Dehalogenase activity was detected with 1,3-dibromopropane as substrate, with steady-state kinetic parameters typical of HLDs (K(m) = 0.24 ± 0.05 mM, k(cat) = 2.4 ± 0.1 s(-1) ). The 2.2-Å crystal structure of DmmA revealed a fold and active site similar to other HLDs, but with a substantially larger active site binding pocket, suggestive of an ability to act on bulky substrates. This enhanced cavity was shown to accept a range of linear and cyclic substrates, suggesting that DmmA will contribute to the expanding industrial applications of HLDs.
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Affiliation(s)
- Jennifer J Gehret
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA
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34
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Wu TH, Huang CH, Ko TP, Lai HL, Ma Y, Chen CC, Cheng YS, Liu JR, Guo RT. Diverse substrate recognition mechanism revealed by Thermotoga maritima Cel5A structures in complex with cellotetraose, cellobiose and mannotriose. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1832-40. [DOI: 10.1016/j.bbapap.2011.07.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 07/02/2011] [Accepted: 07/21/2011] [Indexed: 12/01/2022]
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35
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Sundaresan R, Samen U, Ponnuraj K. Expression, purification, crystallization and preliminary X-ray diffraction studies of the human keratin 4-binding domain of serine-rich repeat protein 1 from Streptococcus agalactiae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1582-5. [PMID: 22139172 PMCID: PMC3232145 DOI: 10.1107/s1744309111040413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 09/30/2011] [Indexed: 11/10/2022]
Abstract
Serine-rich repeat protein 1 (Srr-1) is a surface protein from Streptococcus agalactiae. A 17 kDa region of this protein has been identified to bind to human keratin 4 (K4) and is termed the Srr-1 K4-binding domain (Srr-1-K4BD). Recombinant Srr-1-K4BD was overexpressed in Escherichia coli BL21 (DE3) cells. Native and selenomethionine-substituted proteins were prepared using Luria-Bertani (LB) and M9 minimal media, respectively. A two-step purification protocol was carried out to obtain a final homogenous sample of Srr-1-K4BD. Crystals of native Srr-1-K4BD were obtained using PEG 3350 as a precipitant. The crystals diffracted to 3.8 Å resolution using synchrotron radiation and belonged to space group P2(1), with unit-cell parameters a = 47.56, b = 59.48, c = 94.71 Å, β = 93.95°.
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Affiliation(s)
- Ramya Sundaresan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Ulrike Samen
- Intercell AG, Campus Vienna Biocenter 3, 1030 Vienna, Austria
| | - Karthe Ponnuraj
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
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36
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Akey DL, Li S, Konwerski JR, Confer LA, Bernard SM, Anzai Y, Kato F, Sherman DH, Smith JL. A new structural form in the SAM/metal-dependent o‑methyltransferase family: MycE from the mycinamicin biosynthetic pathway. J Mol Biol 2011; 413:438-50. [PMID: 21884704 PMCID: PMC3193595 DOI: 10.1016/j.jmb.2011.08.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/16/2011] [Accepted: 08/16/2011] [Indexed: 01/07/2023]
Abstract
O-linked methylation of sugar substituents is a common modification in the biosynthesis of many natural products and is catalyzed by multiple families of S-adenosyl-L-methionine (SAM or AdoMet)-dependent methyltransferases (MTs). Mycinamicins, potent antibiotics from Micromonospora griseorubida, can be methylated at two positions on a 6-deoxyallose substituent. The first methylation is catalyzed by MycE, a SAM- and metal-dependent MT. Crystal structures were determined for MycE bound to the product S-adenosyl-L-homocysteine (AdoHcy) and magnesium, both with and without the natural substrate mycinamicin VI. This represents the first structure of a natural product sugar MT in complex with its natural substrate. MycE is a tetramer of a two-domain polypeptide, comprising a C-terminal catalytic MT domain and an N-terminal auxiliary domain, which is important for quaternary assembly and for substrate binding. The symmetric MycE tetramer has a novel MT organization in which each of the four active sites is formed at the junction of three monomers within the tetramer. The active-site structure supports a mechanism in which a conserved histidine acts as a general base, and the metal ion helps to position the methyl acceptor and to stabilize a hydroxylate intermediate. A conserved tyrosine is suggested to support activity through interactions with the transferred methyl group from the SAM methyl donor. The structure of the free enzyme reveals a dramatic order-disorder transition in the active site relative to the S-adenosyl-L-homocysteine complexes, suggesting a mechanism for product/substrate exchange through concerted movement of five loops and the polypeptide C-terminus.
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Affiliation(s)
- David L. Akey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Shengying Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | | | - Laura A. Confer
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Steffen M. Bernard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Fumio Kato
- Faculty of Pharmaceutical Sciences, Toho University 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109,Correspondence: (734) 615-9564, Fax: (734) 763-6492
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37
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Crystal structure of a copper-transporting PIB-type ATPase. Nature 2011; 475:59-64. [PMID: 21716286 DOI: 10.1038/nature10191] [Citation(s) in RCA: 242] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 05/11/2011] [Indexed: 01/19/2023]
Abstract
Heavy-metal homeostasis and detoxification is crucial for cell viability. P-type ATPases of the class IB (PIB) are essential in these processes, actively extruding heavy metals from the cytoplasm of cells. Here we present the structure of a PIB-ATPase, a Legionella pneumophila CopA Cu(+)-ATPase, in a copper-free form, as determined by X-ray crystallography at 3.2 Å resolution. The structure indicates a three-stage copper transport pathway involving several conserved residues. A PIB-specific transmembrane helix kinks at a double-glycine motif displaying an amphipathic helix that lines a putative copper entry point at the intracellular interface. Comparisons to Ca(2+)-ATPase suggest an ATPase-coupled copper release mechanism from the binding sites in the membrane via an extracellular exit site. The structure also provides a framework to analyse missense mutations in the human ATP7A and ATP7B proteins associated with Menkes' and Wilson's diseases.
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38
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Whicher JR, Florova G, Sydor PK, Singh R, Alhamadsheh M, Challis GL, Reynolds KA, Smith JL. Structure and function of the RedJ protein, a thioesterase from the prodiginine biosynthetic pathway in Streptomyces coelicolor. J Biol Chem 2011; 286:22558-69. [PMID: 21543318 PMCID: PMC3121400 DOI: 10.1074/jbc.m110.213512] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prodiginines are a class of red-pigmented natural products with immunosuppressant, anticancer, and antimalarial activities. Recent studies on prodiginine biosynthesis in Streptomyces coelicolor have elucidated the function of many enzymes within the pathway. However, the function of RedJ, which was predicted to be an editing thioesterase based on sequence similarity, is unknown. We report here the genetic, biochemical, and structural characterization of the redJ gene product. Deletion of redJ in S. coelicolor leads to a 75% decrease in prodiginine production, demonstrating its importance for prodiginine biosynthesis. RedJ exhibits thioesterase activity with selectivity for substrates having long acyl chains and lacking a β-carboxyl substituent. The thioesterase has 1000-fold greater catalytic efficiency with substrates linked to an acyl carrier protein (ACP) than with the corresponding CoA thioester substrates. Also, RedJ strongly discriminates against the streptomycete ACP of fatty acid biosynthesis in preference to RedQ, an ACP of the prodiginine pathway. The 2.12 Å resolution crystal structure of RedJ provides insights into the molecular basis for the observed substrate selectivity. A hydrophobic pocket in the active site chamber is positioned to bind long acyl chains, as suggested by a long-chain ligand from the crystallization solution bound in this pocket. The accessibility of the active site is controlled by the position of a highly flexible entrance flap. These data combined with previous studies of prodiginine biosynthesis in S. coelicolor support a novel role for RedJ in facilitating transfer of a dodecanoyl chain from one acyl carrier protein to another en route to the key biosynthetic intermediate 2-undecylpyrrole.
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Affiliation(s)
- Jonathan R Whicher
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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39
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Ebbes M, Bleymüller WM, Cernescu M, Nölker R, Brutschy B, Niemann HH. Fold and function of the InlB B-repeat. J Biol Chem 2011; 286:15496-506. [PMID: 21345802 DOI: 10.1074/jbc.m110.189951] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Host cell invasion by the facultative intracellular pathogen Listeria monocytogenes requires the invasion protein InlB in many cell types. InlB consists of an N-terminal internalin domain that binds the host cell receptor tyrosine kinase Met and C-terminal GW domains that bind to glycosaminoglycans (GAGs). Met binding and activation is required for host cell invasion, while the interaction between GW domains and GAGs enhances this effect. Soluble InlB elicits the same cellular phenotypes as the natural Met ligand hepatocyte growth factor/scatter factor (HGF/SF), e.g. cell scatter. So far, little is known about the central part of InlB, the B-repeat. Here we present a structural and functional characterization of the InlB B-repeat. The crystal structure reveals a variation of the β-grasp fold that is most similar to small ubiquitin-like modifiers (SUMOs). However, structural similarity also suggests a potential evolutionary relation to bacterial mucin-binding proteins. The B-repeat defines the prototype structure of a hitherto uncharacterized domain present in over a thousand bacterial proteins. Generally, this domain probably acts as a spacer or a receptor-binding domain in extracellular multi-domain proteins. In cellular assays the B-repeat acts synergistically with the internalin domain conferring to it the ability to stimulate cell motility. Thus, the B-repeat probably binds a further host cell receptor and thereby enhances signaling downstream of Met.
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Affiliation(s)
- Maria Ebbes
- Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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40
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Kim KH, Ha BH, Kim SJ, Hong SK, Hwang KY, Kim EE. Crystal structures of Enoyl-ACP reductases I (FabI) and III (FabL) from B. subtilis. J Mol Biol 2010; 406:403-15. [PMID: 21185310 DOI: 10.1016/j.jmb.2010.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/25/2010] [Accepted: 12/01/2010] [Indexed: 12/22/2022]
Abstract
Enoyl-[acyl carrier protein] (ACP) reductase (ENR) is a key enzyme in type II fatty acid synthesis that catalyzes the last step in each elongation cycle. Therefore, it has been considered as a target for antibiotics. However, recent studies indicate that some pathogens have more than one ENR; in particular, Bacillus subtilis has two ENRs, FabI and FabL. The crystal structures of the ternary complexes of BsFaBI and BsFabL are found as a homotetramer showing the same overall structure despite a sequence identity of only 24%. The positions of the catalytic dyad of Tyr-(Xaa)(6)-Lys in FabL are almost identical to that of FabI, but a detailed structural analysis shows that FabL shares more structural similarities with FabG and other members of the SDR (short-chain alcohol dehydrogenase/reductase) family. The apo FabL structure shows significantly different conformations at the cofactor and the substrate-binding regions, and this resulted in a totally different tetrameric arrangement reflecting the flexibility of these regions in the absence of the cofactor and substrate/inhibitor.
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Affiliation(s)
- Kook-Han Kim
- Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolkok-dong, Sungbuk-gu, Seoul 136-791, South Korea
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41
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Bröcker MJ, Schomburg S, Heinz DW, Jahn D, Schubert WD, Moser J. Crystal structure of the nitrogenase-like dark operative protochlorophyllide oxidoreductase catalytic complex (ChlN/ChlB)2. J Biol Chem 2010; 285:27336-27345. [PMID: 20558746 PMCID: PMC2930732 DOI: 10.1074/jbc.m110.126698] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/15/2010] [Indexed: 11/06/2022] Open
Abstract
During (bacterio)chlorophyll biosynthesis of many photosynthetically active organisms, dark operative protochlorophyllide oxidoreductase (DPOR) catalyzes the two-electron reduction of ring D of protochlorophyllide to form chlorophyllide. DPOR is composed of the subunits ChlL, ChlN, and ChlB. Homodimeric ChlL(2) bearing an intersubunit [4Fe-4S] cluster is an ATP-dependent reductase transferring single electrons to the heterotetrameric (ChlN/ChlB)(2) complex. The latter contains two intersubunit [4Fe-4S] clusters and two protochlorophyllide binding sites, respectively. Here we present the crystal structure of the catalytic (ChlN/ChlB)(2) complex of DPOR from the cyanobacterium Thermosynechococcus elongatus at a resolution of 2.4 A. Subunits ChlN and ChlB exhibit a related architecture of three subdomains each built around a central, parallel beta-sheet surrounded by alpha-helices. The (ChlN/ChlB)(2) crystal structure reveals a [4Fe-4S] cluster coordinated by an aspartate oxygen alongside three cysteine ligands. Two equivalent substrate binding sites enriched in aromatic residues for protochlorophyllide substrate binding are located at the interface of each ChlN/ChlB half-tetramer. The complete octameric (ChlN/ChlB)(2)(ChlL(2))(2) complex of DPOR was modeled based on the crystal structure and earlier functional studies. The electron transfer pathway via the various redox centers of DPOR to the substrate is proposed.
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Affiliation(s)
- Markus J Bröcker
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Sebastian Schomburg
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Dirk W Heinz
- Division of Structural Biology, Helmholtz-Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | - Wolf-Dieter Schubert
- Division of Structural Biology, Helmholtz-Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany; Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa.
| | - Jürgen Moser
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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42
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Mantri M, Krojer T, Bagg EA, Webby CA, Butler DS, Kochan G, Kavanagh KL, Oppermann U, McDonough MA, Schofield CJ. Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6. J Mol Biol 2010; 401:S0022-2836(10)00558-9. [PMID: 20685276 DOI: 10.1016/j.jmb.2010.05.054] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/21/2010] [Accepted: 05/22/2010] [Indexed: 10/19/2022]
Abstract
Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl residues in arginine-serine-rich domains of RNA-splicing-related proteins. We report crystallographic studies on the catalytic domain of JMJD6 in complex with Ni(II) substituting for Fe(II). Together with mutational studies, the structural data suggest how JMJD6 binds its lysyl residues such that it can catalyse C-5 hydroxylation rather than N(varepsilon)-demethylation, as for analogous enzymes.
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Affiliation(s)
- Monica Mantri
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, Schmelz S, Dorward M, Zawadzki M, Cozens C, Falconer H, Powers H, Overton IM, van Niekerk CAJ, Peng X, Patel P, Garrett RA, Prangishvili D, Botting CH, Coote PJ, Dryden DTF, Barton GJ, Schwarz-Linek U, Challis GL, Taylor GL, White MF, Naismith JH. The Scottish Structural Proteomics Facility: targets, methods and outputs. ACTA ACUST UNITED AC 2010; 11:167-80. [PMID: 20419351 PMCID: PMC2883930 DOI: 10.1007/s10969-010-9090-y] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 04/06/2010] [Indexed: 12/19/2022]
Abstract
The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.
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Affiliation(s)
- Muse Oke
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Lester G. Carter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Stanford Synchrotron Radiation Light Source, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025 USA
| | - Kenneth A. Johnson
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: The Norwegian Structural Biology Centre, University of Tromsø, 9037 Tromsø, Norway
| | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stephen A. McMahon
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Xuan Yan
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Melina Kerou
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Nadine D. Weikart
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Faculty of Chemistry, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Nadia Kadi
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
- Present Address: Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, Surrey, SM2 5NG UK
| | - Md. Arif Sheikh
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stefan Schmelz
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Mark Dorward
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Division of Signal Transduction Therapy, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Michal Zawadzki
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, Berkshire, RG42 6EY UK
| | - Christopher Cozens
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
| | - Helen Falconer
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Institute of Structural and Molecular Biology, Edinburgh University, Kings Buildings, Edinburgh, EH9 3JR UK
| | - Helen Powers
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Ian M. Overton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
- Present Address: MRC Human Genetics Unit, Crewe Road South, Edinburgh, EH4 2XU UK
| | - C. A. Johannes van Niekerk
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Xu Peng
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Prakash Patel
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Roger A. Garrett
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | | | - Catherine H. Botting
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Peter J. Coote
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - David T. F. Dryden
- EaStChem School of Chemistry, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JJ UK
| | - Geoffrey J. Barton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | | | - Garry L. Taylor
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Malcolm F. White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
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Crystal structures of dehydratase domains from the curacin polyketide biosynthetic pathway. Structure 2010; 18:94-105. [PMID: 20152156 DOI: 10.1016/j.str.2009.10.018] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 09/09/2009] [Accepted: 10/30/2009] [Indexed: 11/23/2022]
Abstract
Modular polyketide synthases (PKS) make novel natural products through a series of preprogrammed chemical steps catalyzed by an assembly line of multidomain modules. Each assembly-line step involves unique extension and modification reactions, resulting in tremendous diversity of polyketide products. Dehydratase domains catalyze formation of an alpha,beta-double bond in the nascent polyketide intermediate. We present crystal structures of the four dehydratase domains from the curacin A PKS. The catalytic residues and substrate binding site reside in a tunnel within a single monomer. The positions of the catalytic residues and shape of the substrate tunnel explain how chirality of the substrate hydroxyl group may determine the configuration of the product double bond. Access to the active site may require opening the substrate tunnel, forming an open trench. The arrangement of monomers within the dimer is consistent among PKS dehydratases and differs from that seen in the related mammalian fatty acid synthases.
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45
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Wood CS, Schmitz KR, Bessman NJ, Setty TG, Ferguson KM, Burd CG. PtdIns4P recognition by Vps74/GOLPH3 links PtdIns 4-kinase signaling to retrograde Golgi trafficking. J Cell Biol 2009; 187:967-75. [PMID: 20026658 PMCID: PMC2806290 DOI: 10.1083/jcb.200909063] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Targeting and retention of resident integral membrane proteins of the Golgi apparatus underly the function of the Golgi in glycoprotein and glycolipid processing and sorting. In yeast, steady-state Golgi localization of multiple mannosyltransferases requires recognition of their cytosolic domains by the peripheral Golgi membrane protein Vps74, an orthologue of human GOLPH3/GPP34/GMx33/MIDAS (mitochondrial DNA absence sensitive factor). We show that targeting of Vps74 and GOLPH3 to the Golgi apparatus requires ongoing synthesis of phosphatidylinositol (PtdIns) 4-phosphate (PtdIns4P) by the Pik1 PtdIns 4-kinase and that modulation of the levels and cellular location of PtdIns4P leads to mislocalization of these proteins. Vps74 and GOLPH3 bind specifically to PtdIns4P, and a sulfate ion in a crystal structure of GOLPH3 indicates a possible phosphoinositide-binding site that is conserved in Vps74. Alterations in this site abolish phosphoinositide binding in vitro and Vps74 function in vivo. These results implicate Pik1 signaling in retention of Golgi-resident proteins via Vps74 and show that GOLPH3 family proteins are effectors of Golgi PtdIns 4-kinases.
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Affiliation(s)
- Christopher S. Wood
- Department of Cell and Developmental Biology, Department of Physiology, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Karl R. Schmitz
- Department of Cell and Developmental Biology, Department of Physiology, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Nicholas J. Bessman
- Department of Cell and Developmental Biology, Department of Physiology, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Thanuja Gangi Setty
- Department of Cell and Developmental Biology, Department of Physiology, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Kathryn M. Ferguson
- Department of Cell and Developmental Biology, Department of Physiology, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Christopher G. Burd
- Department of Cell and Developmental Biology, Department of Physiology, and Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
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46
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Herguedas B, Martínez-Júlvez M, Frago S, Medina M, Hermoso JA. Crystallization and preliminary X-ray diffraction studies of FAD synthetase from Corynebacterium ammoniagenes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1285-8. [PMID: 20054130 PMCID: PMC2802882 DOI: 10.1107/s1744309109044789] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 10/27/2009] [Indexed: 11/10/2022]
Abstract
FAD synthetase from Corynebacterium ammoniagenes (CaFADS), a prokaryotic bifunctional enzyme that catalyses the phosphorylation of riboflavin as well as the adenylylation of FMN, has been crystallized using the hanging-drop vapour-diffusion method at 277 K. Diffraction-quality cubic crystals of native and selenomethionine-labelled (SeMet-CaFADS) protein belonged to the cubic space group P2(1)3, with unit-cell parameters a = b = c = 133.47 A and a = b = c = 133.40 A, respectively. Data sets for native and SeMet-containing crystals were collected to 1.95 and 2.42 A resolution, respectively.
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Affiliation(s)
- Beatriz Herguedas
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Susana Frago
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Juan A. Hermoso
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
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47
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Kinoshita M, Yamane M, Matsunami H, Minamino T, Namba K, Imada K. Purification, crystallization and preliminary X-ray analysis of FliT, a bacterial flagellar substrate-specific export chaperone. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:825-8. [PMID: 19652350 PMCID: PMC2720344 DOI: 10.1107/s1744309109026736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 07/08/2009] [Indexed: 11/10/2022]
Abstract
The assembly process of the bacterial flagellum is coupled to flagellar gene expression. FliT acts not only as a flagellar type III substrate-specific export chaperone for the filament-capping protein FliD but also as a negative regulator that suppresses flagellar gene expression through its specific interaction with the master regulator FlhD(4)C(2) complex. In this study, FliT of Salmonella enterica serovar Typhimurium was expressed, purified and crystallized. Crystals of SeMet FliT were obtained by the sitting-drop vapour-diffusion technique with potassium/sodium tartrate as the precipitant. The crystals grew in the trigonal space group P3(1)21 or P3(2)21 and diffracted to 3.2 A resolution. The anomalous difference Patterson map of the SeMet FliT crystal showed significant peaks in its Harker sections, indicating the usefulness of the derivative data for structure determination.
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Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Midori Yamane
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hideyuki Matsunami
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology, 12-22 Suzaki, Uruma, Okinawa 904-2234, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- PRESTO (Precursory Research for Embryonic Science and Technology), JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumi Imada
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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Wu J, Bu W, Sheppard K, Kitabatake M, Kwon ST, Söll D, Smith JL. Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme. J Mol Biol 2009; 391:703-16. [PMID: 19520089 DOI: 10.1016/j.jmb.2009.06.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 04/16/2009] [Accepted: 06/04/2009] [Indexed: 11/18/2022]
Abstract
Many bacteria form Gln-tRNA(Gln) and Asn-tRNA(Asn) by conversion of the misacylated Glu-tRNA(Gln) and Asp-tRNA(Asn) species catalyzed by the GatCAB amidotransferase in the presence of ATP and an amide donor (glutamine or asparagine). Here, we report the crystal structures of GatCAB from the hyperthermophilic bacterium Aquifex aeolicus, complexed with glutamine, asparagine, aspartate, ADP, or ATP. In contrast to the Staphylococcus aureus GatCAB, the A. aeolicus enzyme formed acyl-enzyme intermediates with either glutamine or asparagine, in line with the equally facile use by the amidotransferase of these amino acids as amide donors in the transamidation reaction. A water-filled ammonia channel is open throughout the length of the A. aeolicus GatCAB from the GatA active site to the synthetase catalytic pocket in the B-subunit. A non-catalytic Zn(2+) site in the A. aeolicus GatB stabilizes subunit contacts and the ammonia channel. Judged from sequence conservation in the known GatCAB sequences, the Zn(2+) binding motif was likely present in the primordial GatB/E, but became lost in certain lineages (e.g., S. aureus GatB). Two divalent metal binding sites, one permanent and the other transient, are present in the catalytic pocket of the A. aeolicus GatB. The two sites enable GatCAB to first phosphorylate the misacylated tRNA substrate and then amidate the activated intermediate to form the cognate products, Gln-tRNA(Gln) or Asn-tRNA(Asn).
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Affiliation(s)
- Jing Wu
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, 48109, USA
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49
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Liu L, O'Grady C, Dalrymple SA, Prasad L, Dmitriev OY, Delbaere LTJ. Crystallization and preliminary X-ray studies of the N-domain of the Wilson disease associated protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:621-4. [PMID: 19478447 DOI: 10.1107/s1744309109017023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 05/05/2009] [Indexed: 11/10/2022]
Abstract
Wilson disease associated protein (ATP7B) is essential for copper transport in human cells. Mutations that affect ATP7B function result in Wilson's disease, a chronic copper toxicosis. Disease-causing mutations within the N-domain of ATP7B (WND) are known to disrupt ATP binding, but a high-resolution X-ray structure of the ATP-binding site has not been reported. The N-domain was modified to delete the disordered loop comprising residues His1115-Asp1138 (WNDDelta(1115-1138)). Unlike the wild-type N-domain, WNDDelta(1115-1138) formed good-quality crystals. Synchrotron diffraction data have been collected from WNDDelta(1115-1138) at the Canadian Light Source. A native WNDDelta(1115-1138) crystal diffracted to 1.7 A resolution and belonged to space group P4(2)2(1)2, with unit-cell parameters a = 39.2, b = 39.2, c = 168.9 A. MAD data were collected to 2.7 A resolution from a SeMet-derivative crystal with unit-cell parameters a = 38.4, b = 38.4, c = 166.7 A. The WNDDelta(1115-1138) structure is likely to be solved by phasing from multiwavelength anomalous diffraction (MAD) experiments.
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Affiliation(s)
- Lili Liu
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada
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50
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Bublitz M, Polle L, Holland C, Heinz DW, Nimtz M, Schubert WD. Structural basis for autoinhibition and activation of Auto, a virulence-associated peptidoglycan hydrolase ofListeria monocytogenes. Mol Microbiol 2009; 71:1509-22. [DOI: 10.1111/j.1365-2958.2009.06619.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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